Quantitative proteomics using the high resolution accurate mass capabilities of the quadrupole-orbitrap mass spectrometer

Bioanalysis

Volumn 6, Issue 16, 2014, Pages 2159-2170

  Gallien, Sebastien ^a   Domon, Bruno ^a  

^a LUXEMBOURG INSTITUTE OF HEALTH   (Luxembourg)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COLLISIONALLY ACTIVATED DISSOCIATION; HIGHER ENERGY COLLISIONAL DISSOCIATION; INFORMATION PROCESSING; ION MONITORING; ION THERAPY; ION TRAP MASS SPECTROMETRY; LIMIT OF QUANTITATION; MASS SPECTROMETER; MONITORING; PARALLEL REACTION MONITORING; PROTEOMICS; QUADRUPOLE MASS SPECTROMETRY; QUADRUPOLE ORBITRAP MASS SPECTROMETER; QUANTITATIVE ANALYSIS; MASS SPECTROMETRY; PROCEDURES;

MASS SPECTROMETRY; PROTEOMICS;

EID: 84908160578     PISSN: 17576180     EISSN: 17576199     Source Type: Journal    
DOI: 10.4155/bio.14.115     Document Type: Article

References (33)

1. Nagaraj N, Wisniewski JR, Geiger T et al. Deep proteome and transcriptome mapping of a human cancer cell line. Mol. Syst. Biol. 7, 548 (2011).
2. Schwanhausser B, Busse D, Li N et al. Global quantification of mammalian gene expression control. Nature 473(7347), 337-342 (2011).
3. Thakur SS, Geiger T, Chatterjee B et al. Deep and highly sensitive proteome coverage by LC-MS/MS without prefractionation. Mol. Cell. Proteomics 10(8), M110.003699 (2011).
4. Michalski A, Cox J, Mann M. More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS. J. Proteome Res. 10(4), 1785-1793 (2011).
5. Andrews GL, Simons BL, Young JB, Hawkridge AM, Muddiman DC. Performance characteristics of a new hybrid quadrupole time-of-flight tandem mass spectrometer (TripleTOF 5600). Anal. Chem. 83(13), 5442-5446 (2011).
6. Michalski A, Damoc E, Hauschild JP et al. Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer. Mol. Cell. Proteomics 10(9), M111.011015 (2011).
7. Gillette MA, Carr SA. Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry. Nat. Methods 10(1), 28-34 (2013).
8. Yost RA, Enke CG. Triple quadrupole mass spectrometry for direct mixture analysis and structure elucidation. Anal. Chem. 51(12), 1251-1264 (1979).
9. Gallien S, Duriez E, Domon B. Selected reaction monitoring applied to proteomics. J. Mass Spectrom. 46(3), 298-312 (2011).
10. Picotti P, Aebersold R. Selected reaction monitoringbased proteomics: workflows, potential, pitfalls and future directions. Nat. Methods 9(6), 555-566 (2012).
11. Maccoss MJ, Matthews DE. Quantitative MS for proteomics: teaching a new dog old tricks. Anal. Chem. 77(15), 294A-302A (2005).
12. Gallien S, Peterman S, Kiyonami R et al. Highly multiplexed targeted proteomics using precise control of peptide retention time. Proteomics 12(8), 1122-1133 (2012).
13. Kiyonami R, Schoen A, Prakash A et al. Increased selectivity, analytical precision, and throughput in targeted proteomics. Mol. Cell. Proteomics 10(2), M110.002931 (2011).
14. Domon B, Aebersold R. Options and considerations when selecting a quantitative proteomics strategy. Nat. Biotechnol. 28(7), 710-721 (2010).
15. Rifai N, Gillette MA, Carr SA. Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat. Biotechnol. 24(8), 971-983 (2006).
16. Domon B. Considerations on selected reaction monitoring experiments: implications for the selectivity and accuracy of measurements. Proteomics Clin. Appl. 6(11-12), 609-614 (2012).
17. Gallien S, Duriez E, Crone C, Kellmann M, Moehring T, Domon B. Targeted proteomic quantification on quadrupole-orbitrap mass spectrometer. Mol. Cell. Proteomics 11(12), 1709-1723 (2012).
18. Kelstrup CD, Young C, Lavallee R, Nielsen ML, Olsen JV. Optimized fast and sensitive acquisition methods for shotgun proteomics on a quadrupole Orbitrap mass spectrometer. J. Proteome Res. 11(6), 3487-3437 (2012).
19. Peterson AC, Russell JD, Bailey DJ, Westphall MS, Coon JJ. Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics. Mol. Cell. Proteomics 11(11), 1475-1488 (2012).
20. Gallien S, Bourmaud A, Kim S, Domon B. Technical consideration for large-scale parallel reaction monitoring analysis. J. Proteomics 100, 147-159 (2013).
21. Gallien S, Duriez E, Demeure K, Domon B. Selectivity of LC-MS/MS analysis: implication for proteomics experiments. J. Proteomics 81, 148-158 (2013).
22. Bourmaud A, Gallien S, Domon B. High resolution/accurate mass targeted proteomics. In: Quantitative Proteomics. Royal Society of Chemistry, London, UK (2014).
23. Diedrich JK, Pinto AF, Yates JR. Energy dependence of HCD on peptide fragmentation: stepped collisional energy finds the sweet spot. J. Am. Soc. Mass Spectrom. 24 (11), 1690-1699 (2013).
24. Bensimon A, Heck AJ, Aebersold R. Mass spectrometrybased proteomics and network biology. Ann. Rev. Biochem. 81, 379-405 (2012).
25. Jaffe JD, Keshishian H, Chang B, Addona TA, Gillette MA, Carr SA. Accurate inclusion mass screening: a bridge from unbiased discovery to targeted assay development for biomarker verification. Mol. Cell. Proteomics 7(10), 1952-1962 (2008).
26. Schmidt A, Gehlenborg N, Bodenmiller B et al. An integrated, directed mass spectrometric approach for indepth characterization of complex peptide mixtures. Mol. Cell. Proteomics 7(11), 2138-2150 (2008).
27. Domon B, Broder S. Implications of new proteomics strategies for biology and medicine. J. Proteome Res. 3(2), 253-260 (2004).
28. Panchaud A, Scherl A, Shaffer SA et al. Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean. Anal. Chem. 81(15), 6481-6488 (2009).
29. Venable JD, Dong MQ, Wohlschlegel J, Dillin A, Yates JR. Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat. Methods 1(1), 39-45 (2004).
30. Gillet LC, Navarro P, Tate S et al. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol. Cell. Proteomics 11(6), O111.016717 (2012).
31. Silva JC, Gorenstein MV, Li GZ, Vissers JP, Geromanos SJ. Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition. Mol. Cell. Proteomics 5(1), 144-156 (2006).
32. Geiger T, Cox J, Mann M. Proteomics on an Orbitrap benchtop mass spectrometer using all-ion fragmentation. Mol. Cell. Proteomics 9(10), 2252-2261 (2010).
33. Egertson JD, Kuehn A, Merrihew GE et al. Multiplexed MS/MS for improved data-independent acquisition. Nat. Meth. 10(8), 744-746 (2013).